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- PDB-8x22: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:dGT... -

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Basic information

Entry
Database: PDB / ID: 8x22
TitleHIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:dGTP ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • Pol protein (Fragment)
KeywordsTRANSFERASE / reverse transcriptase / HIV-1 / HBV / drug resistance / nucleoside analogue
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsYasutake, Y. / Hattori, S.I. / Mitsuya, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0310113 Japan
CitationJournal: Sci Rep / Year: 2024
Title: Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations.
Authors: Yasutake, Y. / Hattori, S.I. / Kumamoto, H. / Tamura, N. / Maeda, K. / Mitsuya, H.
History
DepositionNov 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pol protein (Fragment)
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: Pol protein (Fragment)
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,82616
Polymers255,2116
Non-polymers1,61610
Water8,161453
1
A: Pol protein (Fragment)
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4138
Polymers127,6053
Non-polymers8085
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-49 kcal/mol
Surface area46260 Å2
MethodPISA
2
C: Pol protein (Fragment)
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4138
Polymers127,6053
Non-polymers8085
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-52 kcal/mol
Surface area46910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.227, 285.227, 96.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Pol protein (Fragment)


Mass: 64019.363 Da / Num. of mol.: 2 / Mutation: L74V, Y115F, F116Y, Q151M, C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 463 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 127828 / % possible obs: 100 % / Redundancy: 5.5 % / Rrim(I) all: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2.31→2.35 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6352 / Rrim(I) all: 0.926 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDN

6kdn


Resolution: 2.31→48.811 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 6481 5.07 %
Rwork0.1825 --
obs0.1844 127817 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→48.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15688 1495 100 453 17736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817888
X-RAY DIFFRACTIONf_angle_d0.93424601
X-RAY DIFFRACTIONf_dihedral_angle_d24.3426826
X-RAY DIFFRACTIONf_chiral_restr0.0582666
X-RAY DIFFRACTIONf_plane_restr0.0052833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.33630.30272120.26524066X-RAY DIFFRACTION100
2.3363-2.36370.27382130.25814060X-RAY DIFFRACTION100
2.3637-2.39260.3322020.24864092X-RAY DIFFRACTION100
2.3926-2.42280.28871950.24364028X-RAY DIFFRACTION100
2.4228-2.45470.29142400.23514072X-RAY DIFFRACTION100
2.4547-2.48840.27022480.23893977X-RAY DIFFRACTION100
2.4884-2.52390.28932270.23444035X-RAY DIFFRACTION100
2.5239-2.56160.30161970.22844034X-RAY DIFFRACTION100
2.5616-2.60160.29472340.22834043X-RAY DIFFRACTION100
2.6016-2.64420.27331870.23264061X-RAY DIFFRACTION100
2.6442-2.68980.27312250.22114049X-RAY DIFFRACTION100
2.6898-2.73870.25071870.22224069X-RAY DIFFRACTION100
2.7387-2.79140.262170.21684047X-RAY DIFFRACTION100
2.7914-2.84840.24262200.21534051X-RAY DIFFRACTION100
2.8484-2.91030.29132220.21514018X-RAY DIFFRACTION100
2.9103-2.9780.26422450.21524010X-RAY DIFFRACTION100
2.978-3.05250.25572420.2134022X-RAY DIFFRACTION100
3.0525-3.1350.24661850.20224070X-RAY DIFFRACTION100
3.135-3.22720.24272440.19574018X-RAY DIFFRACTION100
3.2272-3.33140.22872020.19134066X-RAY DIFFRACTION100
3.3314-3.45040.22122220.18474006X-RAY DIFFRACTION100
3.4504-3.58850.242170.18264081X-RAY DIFFRACTION100
3.5885-3.75180.20992070.17584027X-RAY DIFFRACTION100
3.7518-3.94950.19732360.16594032X-RAY DIFFRACTION100
3.9495-4.19680.19462180.15584051X-RAY DIFFRACTION100
4.1968-4.52060.15832100.14914060X-RAY DIFFRACTION100
4.5206-4.97520.18922140.1454019X-RAY DIFFRACTION100
4.9752-5.69410.17482100.15664067X-RAY DIFFRACTION100
5.6941-7.17040.20052090.17294042X-RAY DIFFRACTION100
7.1704-48.8110.17471940.15764063X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16630.0401-0.60550.51-0.10492.2931-0.14050.00760.0159-0.02430.0347-0.1050.1999-0.01160.050.2498-0.00990.03910.3275-0.06970.3701178.7951276.5427-146.9215
22.6770.64040.18651.05620.4261.5794-0.21250.4010.2022-0.19940.03860.3334-0.1176-0.59020.17540.31460.0185-0.03770.663-0.050.4858146.5634277.3154-156.0124
31.2355-0.1773-0.34423.151.09483.1126-0.2389-0.1129-0.3724-0.27440.04660.1620.2194-0.33580.14870.3283-0.04180.08060.4156-0.03030.4118175.2861265.3051-148.5189
41.37320.1083-0.15040.9143-0.38440.9985-0.01950.1630.1542-0.1050.04370.1106-0.0545-0.0675-0.03090.2673-0.02410.03480.35960.00930.3262211.835282.6875-183.6973
50.7278-0.2626-0.01541.5286-0.61531.08170.02810.02520.0133-0.0807-0.0057-0.08230.05340.2524-0.00810.2683-0.02320.04560.4230.00750.3619239.4402263.5555-182.4159
63.13880.48830.41621.8304-0.39262.66960.16420.503-0.2032-0.1326-0.36770.04020.52280.10920.21190.4251-0.00310.0840.4298-0.02520.3183208.1283274.612-191.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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